Our company takes PDFs from magazine publishers and uses proprietary software to convert to PDFs to SWF, PNG and JPG for different Web delivery channels. The problem I run into is the occasional page where the graphic designer used many layers, and I have to take the PDF they gave us and do custom Preflight work to yield a PDF that won't cause our software to choke. Typically I'll choose to output a version as PDF/X-1a. This will do some cleanup like Remove Artbox, Flatten transparency, Discard form objects, Discard external cross references, Remove alternate images, Remove document structure compression, Recompress LZW as ZIP, etc. Despite action names that suggest Acrobat is taking out unnecessary things, it's not unusual for file size to go from 220 KB to 7.4 MB. That's a problem because even though this creates a PDF that is more likely to look normal after conversion to images, those images may be so large that download is slow. If I take that PDF I just made and run the Fixup Flatten transparency (high resolution), file size will drop to about 5.9 MB (these sizes are a test I ran for this post).
My first question concerns the PDF/X-1a version. Why does taking stuff out cause the size to mushroom?
Second question, if PDF/X1-a flattened the file, why am I getting any change at all when I run the fixup on the PDF I got after I ran that first step?
Flattening should be expected to make files bigger, much bigger in the worst case. It is rarely a way to reduce size, though sometimes it will be - it all depends on what is in the file.
An example where it could reduce size is where a series of images are overlayed transparently. This would end up being a single one. There may be cases where lots of layers get consolidated into something simpler, but if the layers were vector and the result is raster it won't.
So, flattening might be a useful tool, but it's best to try it and test the result.
Better still to stop the proprietary software from choking... !
By the way, I can't think why flattening a second time should do anything either.
You should probably be using Audit Space Usage before deciding what to do (and also to see what happened in this case).
Are you doing a Save As rather than a Save after you do the work. The Save keeps all of the changed items. Save As clears the old stuff out of the file. I am not sure with preflight, but worth a try.